Gene loci information

Transcript annotation

  • This transcript has been annotated as L-lactate dehydrogenase.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g7339 g7339.t30 isoform g7339.t30 23113428 23114000
chr_2 g7339 g7339.t30 exon g7339.t30.exon1 23113428 23113670
chr_2 g7339 g7339.t30 cds g7339.t30.CDS1 23113429 23113670
chr_2 g7339 g7339.t30 exon g7339.t30.exon2 23113728 23114000
chr_2 g7339 g7339.t30 cds g7339.t30.CDS2 23113728 23113995
chr_2 g7339 g7339.t30 TSS g7339.t30 23114705 23114705
chr_2 g7339 g7339.t30 TTS g7339.t30 NA NA

Sequences

>g7339.t30 Gene=g7339 Length=516
ATCAAATGTTCCAAGCAGTCGCTGAGGATGTGGACTCAAAATCGTCAAATAAAGTCACCG
TTGTCGGAATCGGAGCTGTTGGAATGGCTGCCGCTTTCTCTATTTTGGCTCAAAATGTTT
CAAGTGACGTTGCTCTCATCGATATGTTTGAGAACAAATTGAAAGGAGAGATGATGGATT
TGCAACACGGATCTAACTTTTTGAAGAATGCTAAAATTTCTGCTAGTACTGATTTGTCAG
TCTCTGCTAATTCACGTTTAATCATTGTTACCGCTGGTGTACGCCAGAAGGAAGGCGAGT
CACGTTTGGATTTAGTTCAACGTAATGCAGACATCATGAAGAATTTGATTCCAAAACTCG
TCGAATACAGTCCTGATACTACACTTTTGATTGTCTCAAATCCATGTGATATCTTGACAT
ATGTTGCATGGAAATTATCAGGATTGCCTAAGAACAGAGTTATTGGATCAGGAACTAATT
TGGACTCATCTCGTTTCCGTTTCTTGCTTGCTCAAC

>g7339.t30 Gene=g7339 Length=170
MFQAVAEDVDSKSSNKVTVVGIGAVGMAAAFSILAQNVSSDVALIDMFENKLKGEMMDLQ
HGSNFLKNAKISASTDLSVSANSRLIIVTAGVRQKEGESRLDLVQRNADIMKNLIPKLVE
YSPDTTLLIVSNPCDILTYVAWKLSGLPKNRVIGSGTNLDSSRFRFLLAQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g7339.t30 Gene3D G3DSA:3.40.50.720 - 1 156 1.1E-64
2 g7339.t30 PANTHER PTHR43128 L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+)) 2 170 4.1E-78
4 g7339.t30 PRINTS PR00086 L-lactate dehydrogenase signature 16 40 2.2E-47
6 g7339.t30 PRINTS PR00086 L-lactate dehydrogenase signature 41 65 2.2E-47
3 g7339.t30 PRINTS PR00086 L-lactate dehydrogenase signature 128 148 2.2E-47
5 g7339.t30 PRINTS PR00086 L-lactate dehydrogenase signature 152 170 2.2E-47
1 g7339.t30 Pfam PF00056 lactate/malate dehydrogenase, NAD binding domain 16 154 9.2E-46
8 g7339.t30 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 154 3.67E-65
7 g7339.t30 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 17 39 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0019752 carboxylic acid metabolic process BP
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values